On The Other Side
by ShipperWriter
Summary: When Dr. Elizabeth Weir arrives alive and well - and married - in a hidden lab in Atlantis, can the team get her home - if she even wants to go home? Set in S5, shortly after "Ghost in the Machine".
1. Through A Mirror

This is posted second, but this is the first chapter of this story. Got caught up in the Sparky intimate moment in the next chapter and posted that first!

* * *

They could feel the shudders of the City around them.

The Wraith had kept pounding the City, just to the point of the shields failing, and then halted their attack. Just when they thought it was safe to escape through the Stargate, they couldn't dial out. Rodney had murmured something about a Stargate in orbit, and some other things that she wasn't really listening to. All that mattered was that their last option was blocked.

As she slowly roused from her semi-conscious state, Dr. Elizabeth Weir found herself clutching onto a sturdy column in one of the hidden labs, desperately hoping that the other members with her were still safe.

As the smoke from a small electrical fire started to become transparent, she coughed, "Kate? Meyers?"

"I'm here," a small voice replied.

Elizabeth disentangled herself from the steel pole and wound around the wreckage scattered in the lab they had been exploring, just before the Wraith appeared. She found the resident psychiatrist sitting upright, back pressed firmly against the doors leading out.

"You all right?"

Kate Heightmeyer nodded very briefly. "Nothing broken, no horrendous bleeding. The doors are jammed. I can't get them open."

"I'm not sure how much good it would do to us if they _were_ opened," Elizabeth reasoned, looking around for the young lieutenant that had been escorting them, per her husband's request.

Kate sensed who she was looking for. "I think he got trapped on the other side of the doors. I've tried to radio him, but I think they're out."

Just then, the Expedition leader's earpiece crackled. "Elizabeth! 'Lizabeth, where are you?"

"John!"

"Oh, thank God. I couldn't contact Meyers-"

"Kate and I are stuck in a lab in the East Pier, Section 7, Level 25. Meyers was standing guard outside the door, but after the first blast, they're sealed. We can't get out."

"Understood. I'm sending a team that way. The 'Gate is still blocked, we can't dial out. I've ordered all personnel to try and find another way out, no matter what."

Elizabeth frowned in confusion. "What do you mean, _you've_ ordered? Where's Marshall?"

She heard a heavy sigh. "Sumner's dead. He was in a jumper trying to hold off the darts."

Elizabeth felt her legs go weak under her. Her military commander, the man who had learned to work hand in hand with her, was gone. And now, her husband was technically in charge. She both feared and anticipated this day at the same time.

She put her guard back up immediately, and got to business. "What about the Athosians on the mainland?"

"We couldn't get to them before the attack started. In any case, if we flew a jumper to the mainland, it would alert the Wraith that they're there. I radioed Teyla and told her to lay low, we'd get to them eventually. You know her. She handles the Wraith way better than us."

She smirked. "True."

"All right, you and Kate are okay?"

"Just a couple scrapes, but otherwise, we're fine."

"Okay. Go ahead and keep searching the room. If you find a way out, take it. Right now, it's kinda hard to round everyone up together."

"John."

"Yeah."

"If the Wraith penetrate the 'Gate room, or the control room-"

"The auto destruct is armed. We won't let them find out about Earth."

"John!"

"I have the remote detonator. I'll only use it if I have to."

She moaned, grieved that she could read between the lines so well. She wasn't going to see her husband again. Who knew if she would ever hear his voice again?

She heard a heavy sigh on the other end. "I love you, 'Lizabeth."

"I love you too, John. Be safe," she told him in a quiet voice, uncertain where it had come from.

He broke the connection and she wanted to slump against the wall, burst out into tears and not even bother trying to find a way out. What was the use?

"C'mon, Elizabeth, we need to get out of here."

Her heavy green eyes met Kate's, and instantly felt a wave of relief sweep over her. At least she wasn't completely alone in this.

* * *

Dr. Rodney McKay and Dr. Radek Zelenka were sweeping the rooms in the lower level. Radek was murmuring something in Czech, and Rodney wasn't saying anything. His jaw was almost to the floor as his eyes widened. "Oh wow," was all he could manage when he finally found his voice again.

"It looks like the props storehouse for Atlantis," Radek said, smiling at the fit description.

A wealth of new technology lay in front of them, some things that they couldn't even imagine what use they would have. It indeed looked like props. Why did the Ancients invent them? What were they for? How did they work?

Radek walked down one aisle, slowly, looking as if he were categorizing everything by the intensity of his stare. Rodney let out another amazed, "Wow," and touched his comm piece. "Control room, this is McKay, come in?"

"We read you, McKay, where are you?" John Sheppard asked.

"Um, well, Radek and I were surveying some of the labs that we hadn't looked into, yet, and well, one of the rooms that we got into, it's, uh, it's pretty close to the transporter-"

"Rodney, make it quick, or I'm ending this call."

McKay groaned. "Fine. Anyways, we found a treasure trove of what I-" As Radek cleared his throat, he rephrased. "-of what _Radek_ and I believe to be a mass amount of Ancient technology. I want to start-"

One of the devices in the far corner started making noises just as Rodney was talking. He paused, staring at Zelenka in confusion. "Wha - what was that? Radek, what did you do?"

"I did nothing," Radek swore, raising his hands in front of him.

"McKay, what's going on?"

"I don't know, just give me a minute!"

The two scientists proceeded carefully towards the location of the ruckus and discovered what appeared to be a full length mirror nestled in the corner, glimmering on its surface. Yet the reflection didn't show them at all; it showed a dark room, full of smoke and sparks flying.

"Sheppard, you better get down here. Something's happening." He tapped his earpiece, ending the conversation, and consulted the tablet in his hands. "Radek, what do you make of this?" he asked, looking down as the Czech scientist stopped walking next to him.

Radek didn't reply directly; all Rodney heard was a gasp, followed by more soft cursing in his native language.

Rodney groaned, rolling his eyes upwards and glaring at Radek. "Now what?" he asked, exasperated.

His gaze was solidly fixed on the shimmering surface, and Rodney's eyes followed to see something - rather, _someone_ - that he never expected to see again.

Especially after everything that the Expedition had been through.

"Oh my God," was all he could say as he saw the panicked faces of Dr. Kate Heightmeyer and Dr. Elizabeth Weir appear as they touched the surface on their side.

* * *

Teyla had seen Sheppard take off running from the control room and quickly followed him to the transporter. She arrived apparently just after Sheppard had, judging by the gasping and moaning coming out of the colonel's mouth. The transporter doors closed in front of them.

"John, what is the matter?" she asked, standing next to John as he was bent over, hands on his knees, panting.

"I don't know, McKay is exploring the city and found something. The comm got cut off."

As the doors opened once more, he reached for the gun that was holstered at his side. "Just in case," he said, holding his thumb against the safety.

Teyla walked behind him, having left her weapon in the armory, and glanced over his shoulder.

John kept looking at the top of the corridors, trying to find the section numbers, until he found the one that Rodney had previously been exploring. "Rodney?" he called out, holding his gun securely in front of him.

"In here!"

John looked sharply at Teyla. Rodney's voice sounded more panicked than normal. He clicked off the safety and rounded the corner into the room.

He saw the generous amount of devices that Rodney had told him about and knew he was in the right place. He stalked down one of the aisles and saw Rodney and Radek crowded around a glowing item in the corner.

"Rodney?" he called out quietly.

Rodney spun quickly and stared at him, a look of disbelief plastered on his face. Behind him, the device seemed to power off, and he heard a stifled sob behind the men.

There was just enough space between them for John to see though, and he almost felt faint at the sight, yet tightened his grip on his gun.

"Elizabeth."

She turned around, and stared at John. "John," she said, her voice seeking comfort.

John narrowed his eyes. They widened again as Teyla moved forward next to him, looking at the fourth person they encountered that John's hazel eyes seemed to have missed.

"Kate?"

The deceased psychiatrist smiled kindly at them. "John. Teyla."

John's eyes widened again. He felt his pulse quicken. Something wasn't right.

"Rodney? What's going on?" John asked, glancing sideways at him as he slowly started to lower his firearm.

Elizabeth Weir glanced up at him. "I think we can explain better."

John nodded wearily at her. "First things first. Let's get you to the infirmary, and make sure you are who you say you are."

Elizabeth and Kate nodded at him.

* * *

Elizabeth sat on the exam bed, wringing her hands nervously as Jennifer stood in front of her, checking off items on her clipboard. "All right, bloodwork is completely normal." She flipped the pages back to the front. Looking at the visitor with a anxious smile, "As far as I'm concerned, you are Dr. Elizabeth Weir."

Elizabeth nodded her thanks, knowing they would do whatever was needed to ensure the safety of Atlantis. She noted Rodney's awestruck smile, probably amazed at the new technology that they had discovered. Teyla was giving her most reassuring smile. And John stood near the exit to the infirmary, looking as if he were getting ready to bolt.

Sitting on the bed next to her, Dr. Kate Heightmeyer sighed. "So we are who we are. What's next?"

John walked up to the pair, arms crossed. "Why did you come here?"

Elizabeth glanced at the woman sitting across from her. "Our city had been under siege by the Wraith for months. Finally, our last ZPM was depleted, the drones ran out, and the shields failed. We couldn't protect ourselves anymore. We tried to dial the 'Gate to any address that wasn't in Wraith territory, but we couldn't dial out. Rodney assumed that the ships in orbit had a Stargate aboard and it was active, and being in such close proximity, we were trapped."

Teyla looked between the women. "We were under siege by the Wraith within our first year on Atlantis. Did you not experience that?"

"We did," Kate informed her, standing from the bed to stretch her legs gently. "We successfully made it through. The first time, the second time, the third time, and so on."

"Wa - wait," Rodney interjected, holding up his hand. "Exactly how many sieges have you had?"

Elizabeth stared down. "We'd lost count. They were so ruthless, so determined to destroy us."

"They didn't want to go to Earth?" John asked, starting to appear confused.

Elizabeth raised an eyebrow. "They didn't know Earth existed. The stories that were circulating were that we were Ancients, trapped in stasis, who had been revived and were reestablishing Atlantis as a base of power in the galaxy. Somehow, they came under the impression that we had a weapon of some type, capable of wiping out the entire race. After they heard that, they didn't bother to stop and ask questions. They continued attacking us until we couldn't defend ourselves anymore."

John nodded. "Yeah, they're not real big on talking."

Elizabeth smiled. "True. In any case, being blocked in the city, we assembled more invasive search teams, trying to find anything in the hidden labs that might help us. Kate and I were in the quadrant where we found the mirror when the shield finally failed."

"What happened to the rest of the Expedition?"

She shook her head sadly, almost overcome with guilt. "Colonel Sumner-"

"_Sumner_?" John spat quickly, eyes narrowed at her.

"Yes," Kate replied. "He's the ranking military off-"

"I know who he is, but … sorry, it's just, in our world, he died shortly after we arrived. He was captured by the Wraith."

"We never personally saw or encountered the Wraith before the sieges started," Elizabeth replied, casting a weary look around the room. "We heard talk of them from the Athosians, and other peoples that we encountered, but never came face to face."

She watched Rodney tap the information into the ever present tablet that he was holding, murmuring quietly, "Well, there's one big difference."

John shook his head. "What happened right before we found you?"

She shook her head in mild shock. "Um, John told me Colonel Sumner had died. Teyla was on the mainland with her people. Kate and I were trapped in a lab, trying to find another way out. We heard the darts flying over head, and then someone over the radio shouted that they were beaming into the city. John was outside the lab, trying to find a way in, when the Wraith found him." She suddenly flinched, and looked around the room at the grim group.

Looking at John's eyes, she saw the familiar hazel that she loved, but there was something else there. Something hidden behind the darkness, something that made her want to run away.

Not breaking eye contact, she gulped. "When we found the mirror, we assumed it was similar to the one that SG-1 had encountered. I suppose we got lucky."

"Yes, it, uh, it seems to follow the same parameters as their quantum mirror, with a few minor variations," Rodney confirmed.

She glanced at Jennifer Keller, leaning again a wall. "Um, Doctor, what are the symptoms of entopic cascade failure?" she asked.

"Sorry?"

"Entopic cascade failure? I'm worried about when it might start affecting me."

Rodney's face scrunched in thought. "Why would you be worried about that?"

"I came through a quantum mirror from another universe. Having two Elizabeth Weirs in one place might be too much," she replied with a slight chuckle.

A deep voice in the group let out a strangled groan. She caught a glimpse of dark, unruly hair making its way through the door out of the infirmary.

She looked back to the small crowd in confusion. "I mean, there are … two Elizabeth's … aren't … there?"

Teyla sighed, Rodney ran a hand over his face, and Jennifer shook her head.

"Oh my God," she replied in realization.

Her counterpart was dead.

She was dead.

That thought scared her more than all the previous sieges she had endured.

No wonder John pulled his gun on her.

_It must break his heart for him to see me_, she silently decided, fingering the ring on her left hand.

* * *

Please review, tell me what you think! Thanks for reading!


	2. Coming to Grips

On The Other Side by ShipperWriter

Summary: When Dr. Elizabeth Weir arrives alive and well - and married - in a hidden lab in Atlantis, how do the team get her home - if she even wants to go home? Set in S5, sometime after all the Franibeth storylines wrapped up on screen.

Disclaimer: I don't own anything. Except whatever I ate to make me dream up this story.

AN: This chapter isn't actually the first chapter, it's probably the second, but it's the chapter I wanted to write first before I forgot it. I'll post the rest of the story soon ... I promise!

* * *

Standing next to the flimsy twin sized bed, Elizabeth stretched in the darkness of the spare quarters that she'd been assigned on Atlantis. They weren't hers. They weren't even for a VIP. She desperately longed for the queen sized bed that she and John shared during their marriage, wishing that she could be with him right now.

But her John had died.

She wasn't even in _her_ Atlantis.

She was in a another place, tragically far away from the comforts of her own home. Every time that she walked past someone who was unaware of her presence, she felt like a dead woman walking. And the more that she continued to think that, she realized it was the truth. At least, it was true for this Atlantis.

Their Elizabeth Weir had sacrificed herself to the Replicators to save her team. To save her people.

To save John.

She almost smirked, knowing that in that respect, they were identical. When it came to John Sheppard, their feelings were mutual. She had known from the moment that she saw the fear, shock, disbelief in his eyes when she reappeared in a hidden lab in the depths of Atlantis.

He was in love with her.

And she was gone.

She sighed, glancing at the door, knowing that at least one Marine stood guard outside.

It wasn't that she was a threat, they had explained to her. It was just to ensure that no harm came to her.

She had wryly made a comment, asking if Kavanaugh was still in the city, knowing full well that he probably wasn't.

A classic Sheppard Smirk pulled at the corner of his mouth, but it faded just as quickly as it had appeared.

As she had been escorted back to the designated room for her earlier that evening, she pondered what was going through his head.

He was thrilled to see her again. Not a Replicator, alive, in the flesh. Even if she was from another reality. Even if she was married to John in her universe. Even if she wasn't wearing her usual red shirt.

But he couldn't let himself get close to her again.

He didn't want to have his heart shattered anymore.

Then her door chimed.

She stood facing the side of her bed, knowing who it was. Her hands ached against the mattress. She only wanted a good night of sleep. Even though she knew that was a pipe dream, being here. So close to him. Given how he had reacted around her, she just wanted to ignore the bell, crawl into bed, and fake her way through a dark night without sleep.

Then he knocked. Through the door, she heard, "Elizabeth. It's me."

_I know_.

Sighing heavily in resignation, she replied, "Come in."

As the doors slid open, she stole a glance in the mirror, positioned just so that she could observe the corridor outside without his knowledge.

The guard that had brought her to these quarters was gone.

It was only John.

She pulled the covers back from the pillow. "Hi," she said awkwardly, still not looking right at him.

"Hey," he replied, just as uneasily, hands stuffed in the pockets of his black workout pants.

She sat on the bed, sliding one leg under the covers, drawing the other up to her chest, hugging it for some semblance of comfort.

John walked a bit closer. "You, uh, you getting ready to go to sleep?" he asked, even though he clearly knew the answer.

"Yeah."

He nodded.

She blinked, trying to force the threatening tears to stay gone, and when her eyes opened again John had taken another step, then another, and another, until he was sitting on the edge of the bed, right in front of her.

She stifled a gasp of shock. "You okay?" he asked softly, trying to make eye contact as hers kept staring down at the bed.

"I'm fine," she said, definitely not believing it herself.

John chuckled. "Liar."

That brought her eyes up. "Excuse me?"

"You-" He abruptly caught himself, letting out a weary sigh. "-Elizabeth Weir is one of the best bluffers I know. But you can't even look me in the eye and tell me that."

So she looked him intently in the eyes. "John." She tilted her head ever so slightly, a smile fluttering briefly on her lips. "I'm fine."

There was that smirk again. "There we go. Much better."

"Sarcasm doesn't become you, Colonel," she replied, feeling the easy conversation starting to fall into place again, until she realized, with a heart stopping thud, that the man sitting next to her wasn't the same one who gave her the silver wedding ring.

Close. Too close.

She pulled back, barely noticeable but it seemed obvious to John. He released an accepting groan as he started to pull back himself, muttering, "All right, then. I'll see you in the morning."

She nodded, then quickly took in the broken man before her.

His ring finger was bare, but she would bet that his wedding band was on his dog tags, hanging over his neck and close to his heart. He didn't have the same scars as her John; there were a few blaring discrepancies between their worlds in regards to the incidents which left his beautiful, tan skin a bit marred. This John seemed to have a few more grey hairs than her husband had, before he died. The same worn, yet friendly wrinkles that were starting to set in around his eyes.

If it hadn't been for the obvious discomfort that he was experiencing due to her presence, she might have never known the difference.

And right then, she felt a twinge of guilt as she started pondering another related topic.

_I wonder if he kisses like John._

She felt like she was cheating on her deceased partner, just to think that.

But before she could control herself, she softly called his name, before he withdrew too far.

"John?"

His seat hadn't even left the bed before he whirled back around, putting his hands around her neck as he kissed her, almost shyly at first, probably feeling the same way that she did. After a few seconds, hours, minutes, weeks, she couldn't tell anymore, the tip of his tongue touched her lower lip, begging for entrance.

She consented.

He carefully explored, just her lips at first, then deeper as his hands wove behind her head, pulling her as close to him as possible without melting into him.

Her mind stopped any lucid thoughts, immediately swimming with _Oh my God, it's just like John_ and _What are you thinking? He's not your husband_ and _I don't care, and apparently, neither does he_.

They pulled back simultaneously, short of breath and trying to gauge the other's reaction.

Their eyes spoke more in one second than they could have out loud.

_Are you sure? You all right?_

_Just kiss me, John._

So he did.

She managed to push the covers aside with the one leg that John wasn't currently shifting his own legs atop of, trying to slide easily down the length of the bed, trying to move further from the edge so John had some room to lay as well.

He didn't need room on the bed; on top of her was seemingly comfortable to both.

She pulled him closer, running her hands up and down his back, sneaking in and out of his shirt, trying to raise it higher with each pass.

John pulled back. "No, 'Lizbeth," he breathed out, running his thumbs over her cheeks as he held her face.

"What?" she asked, face flushed with concern.

He shook his head. "I just - this - it doesn't feel right. You know?"

She moaned. "I know, I know."

He moved to sit up, pulling her shoulders closer as she maneuvered upright as well.

"You're not my wife. And I'm not your husband, as much as I'd like to be."

That made her giggle. Just for a moment.

"Even though, technically, we _are_ married, I don't want to do anything that's gonna make this even more … more-"

"Awkward?" she filled in.

He started to say something, then closed his mouth.

"Yeah, I know."

She felt him shudder as he held her.

"What's wrong?"

She felt him gulp. "The first time after Elizabeth disappeared, the first time that we thought we'd found her, well, actually, she found us - anyhow, when she said that she was a Replicator copy and that it wasn't really her, I started having a hard time believing what she was telling us. I said, 'This is all a little-' and she immediately filled in, 'Strange? Yeah. I know.' And just now, when you said that … it started hurting again," he honestly admitted, pulling the woman in his arms closer to him.

Her head nestled into his shoulder, wanting to put her arms around him and just hold him through the night. They had told her about the previous times that they had encountered her - well, the Elizabeth Weir that belonged to this universe - but she had no clue about how John had dealt with each instance.

"Does it hurt you that I'm here now?" she asked quietly, expecting another honest answer.

"Yes. And no."

"What do you mean?"

"Well, having you here, and not the Elizabeth that I came to Atlantis with, having to go through everything again, it hurts like hell. But on the bright side," he added, gently kissing the top of her head, "at least you're not a Replicator this time around."

She had to laugh at that, if not for the honesty but just to break the tense mood. "That's true. I think."

He gripped her shoulder, before pulling back and taking her in with his eyes. "God, you look just like her. Except for this," he told her as he pointed to a scar that ran down her right inner elbow.

"You - well, my husband - gave that to me."

"I hurt you?" he asked in concern, seeming to not care anymore about the difference between the universes. For all intents and purposes, they were the same people. He was still the same man that Elizabeth had fallen in love with. Just from a slightly different life.

"Not intentionally," she assured him with a small smile. "You are the last person that would ever hurt me."

"Yeah, I'm gonna disagree on that one."

"Why?"

"I'm the one that left you on the Asuran homeworld," he answered simply. "I _was _the last person that hurt you. Literally."

"John. Even though I'm not the one who experienced that, I can tell you, without a doubt, that had I been in her position, I would've ordered you to leave. To save yourself, to save the city, to destroy them. Elizabeth died protecting her people. She saved you, John. To continue beating yourself up about deserting her is pointless. Not to mention stupid."

"You taste just like her," he suddenly interjected.

That statement took her aback. "What?"

"When I kissed you? It was just like kissing my Elizabeth. Maybe, maybe this wasn't a good idea." He started to stand again, Elizabeth jumping from the bed and on his heels as he quickly made his escape to the doors.

"John!"

"Elizabeth-"

She grabbed him by the arm, stopping him in the middle of the room, still closer to the bed than to the door.

"What did you do with your ring?"

"Huh?"

"Your wedding ring. Where is it?"

Glancing down at his chest, he started to pull the chain up, then stopped and just decided to strip his black shirt off.

Just as she had predicted, his ring was on the smaller silver chain, next to his dog tags.

What drew her gaze, however, was a small scar on his chest, just above the chains. She clearly recognized the markings.

"A Wraith fed on you," she murmured, a fact more than a question. Her fingertips reached to it, hesitantly at first, but after an approving nod from John, she traced the outline. "What happened?"

He gave a small shrug. "You know Kolya? The Genii?"

"Unfortunately."

"He kidnapped me a couple years ago. Had a Wraith feed on me and forced you to watch."

She shivered, pulling her hand back, unwillingly picturing what he had said transpired. She had seen too many feedings in her time on Atlantis; all she had to do was see an unfortunate man and replace his head with her husband's. Wrinkles becoming more apparent, larger. Hair slowly turning more salt and pepper. Screaming.

"Oh my God," were the only words of sympathy that she could offer up for him, as well as trying to console herself.

"Well, the Wraith and I worked together to escape, and once we had, he reverse fed on me. Gave me my life back. Became a part-time ally, part-time enemy, full-time pain in the butt after that."

"What was Kolya trying to get?"

"They wanted you to turn Ladon Radim over to him. I was the bargaining chip. And, I found out from a few of the guards, a lot of people in Pegasus thought that we were sleeping together, so they thought it would diminish your determination." He chuckled. "They really didn't know you."

She nodded, starting to feel the awkwardness again.

"Elizabeth."

She glanced up, then down, at him as he bent to retrieve his shirt from the floor.

"Can I stay here? Just to be around?"

"John, I thought you said-"

"I know, I said this wasn't a good idea. But when it comes down to it, I still love you. Even if you aren't the woman I married, you're still the person I loved. And nothing's ever gonna change that. Nothing." He gripped her hands, letting his t-shirt fall abandoned yet again. His hazel eyes, now tranquil, met her green anxious ones.

"How long?"

"I dunno. Sunrise? I have a run-"

"No. I meant, how long until you took your ring off your finger?"

"Oh," he replied clumsily, reaching for the silver band around the chain. "I think, right around the time that we found Carson. Almost a year. When we found him, it was another stab in the heart. People almost started expecting you to show up in another one of Michael's labs, and when Carson saw the ring, he asked me, 'So I take it Elizabeth's doing well?'"

She shuddered in sympathy. "Ouch."

"Yeah. Rodney had to explain to Carson why I walked out of the room so fast. In the back of my mind, the light was always on for her, but as time went on, the light got dimmer and dimmer. The first time, after her copy told me that she had been killed, I sent most of her belongings back to Earth and went to see her mother. When she came back for the last time, I desperately wanted her to stay, almost sent off a requisition for her stuff again. But it still wasn't the same. I was as awkward with her as I was with you."

He took a breath, and glanced back to Elizabeth. "Some days, I still look at my hand, thinking it's still there. But no matter what, it's never leaving me."

"My husband just died. Less than a week ago," she remarked simply.

"I know." He gently kissed her forehead, then met her gaze. "I wish I could say that it gets easier, but it doesn't. You just find new ways to distract yourself, and deal with the pain. Don't take this the wrong way, but I'm jealous of you."

"Jealous?" she asked curiously.

He nodded, seeming to be a hard motion for him. "I didn't find out for sure until just recently. At least you know for certain. You have instant closure. Which, I'm sure, being here with me isn't helping anything."

"Actually, this is helping me the most." She paced away from him, walking to the desk where a few objects that made it through with her now resided, how ever temporary it may be. "Talking to you about all of this … it's almost as if he's here, telling me where to go from here."

John stuffed his hands back in his pockets. "So. Where do you go from here, Elizabeth Weir?"

Elizabeth looked back up at him, feeling as if they were back at square one.

"I am going over there," she said, gesturing at the bed. She pointed back to him. "You can stay, if you want to."

Neither of them said anything else. John leaned over and picked up his t-shirt, folding it messily and laying it on the chair next to the desk. Elizabeth went back to the bed and picked up the covers, putting both legs in this time. As she got comfortable, John sat next to her, kicking off his shoes, mirroring her recline as he lay behind her, almost spooning her to stay on the bed. He wrapped his arms around her waist, and she started to relax, letting all the built up tension escape through a heavy groan.

He kissed the back of her neck, and faintly she heard a "good night" before they both fell asleep.

* * *

TBC ...


	3. Five Weeks Later

**_Five weeks later …_**

Elizabeth awoke one morning and expected to roll over, away from the bright Lantean sunshine beaming into her face, and stare into the smiling eyes of one John Sheppard. Ever since she touched the mirror and left her world behind, they had spent time attempting to determine if there was anything left to return to. But with every passing day, every intense kiss from this John, every smile from the other members, the chances seemed smaller and smaller, and the thought of leaving this Atlantis was almost too much to bear.

As it happened, when she turned over in bed this morning, she found rumpled sheets.

A note lay atop the pillow that John's head normally resided on during the night, along with a single flower, a red wildflower picked from the mainland.

_Hey,_

_Had an early training session with some newbies in the jumpers. Be back around 1000._

_Love you. John._

She smiled, tenderly touching the note that he had written. Their relationship was one that was difficult to define. They were married, but not to each other. The John Sheppard that she had pledged her life to was gone. So it was for him with regards to his Elizabeth. But the person was still alive, and still in love with her.

And she gladly accepted the pure, unselfish, attentive love that he wholeheartedly gave her.

They opened up to each other so much after that first night. They explored their histories, found where events had taken different turns, and came across some actions and behaviors that were almost identical between the timelines.

After the critical eyes of the IOA finally lifted, she was permitted to reenter the city's every day life, even taking on some responsibilities. However, Richard Woolsey had been appointed by the IOA as the Expedition leader, and they made it abundantly clear that just because she had reappeared did not mean that she would be again allowed to lead the city.

Despite Woolsey's attempts to step back and attempt a joint administrative position, the office within the transparent walls overlooking the Stargate remained his.

She was soon allowed to join away teams on first contacts. Her negotiating skills were still over par; eventually her job description became something along the lines of "First Contact Specialist".

Hearing a slight crackling, she picked up the ear piece laying on the nightstand. Upon hearing Major Lorne's gentle reminder of SGA-2 leaving at 1300 hours, she acknowledged him and sighed, removing the ear piece yet again.

Her old life had shattered. So far, this new life was everything that she expected it would be.

So she rose from the warm blankets and made her way to the bathroom, preparing to start her day.

* * *

As John watched the last of the new personnel leave the jumper bay, he took a different path back to his - well, their - quarters.

He hadn't been the first to admit, sharing quarters with Elizabeth was strange, at first. Given everything that she had just been through, he assumed that she wouldn't want anything to do with him. _Constantly seeing the doppelganger of your deceased husband might be a bit too much_, he had sarcastically but logically reasoned with her.

She had answered with a rather mind blowing kiss, assuring him that his presence was vital to her well being.

For the past five weeks, he had eaten breakfast with her, attended senior staff meetings sitting next to her, brought her dinner when she would hole up in her new office, and slept next to her every night.

The cliché, _The more things change, the more they stay the same_, didn't do their present situation justice.

He glanced at his watch as he rounded a corner. He stopped short, racking his mind to remember exactly where he was. He knew this city like the back of his hand, but recent arrivals had gotten assigned new quarters, and he thought one of the resident psychiatrists had obtained a room near here.

His searching gaze came upon Kate Heightmeyer as the doors opened, letting her out of her room. She sighed, then glanced up, having noticed John's presence in the corridor. "Colonel," she greeted with a smile on her face. "How are you today?"

"Never better," he replied, chuckling.

She nodded, mouth still up turned, and motioned to the corridor. "I was just about to get some breakfast. Do you mind if we walk?"

"You're not gonna charge me extra, are you?"

She narrowed her eyes at him as he walked in step next to her. "I'll add it to the bill," she answered seriously.

He frowned, then saw the glimmer of humor in her eyes. "Oh, ha ha."

"So. What's on your mind?"

He shrugged, sliding his hands in his pockets as he suddenly found the flooring in front of him fascinating. "Nothing much." He chuckled inwardly at her ability to turn normal conversation into a therapeutic session.

She tilted her head, accepting his standard response. "How's Elizabeth?"

"Doing great. She's heading off world with Lorne's team this afternoon. Another first contact mission."

"How do you feel about her going on these missions?"

"Fine. I mean, it's preferable to staying in Atlantis, moping around all day," he reasoned, turning briefly to look at her.

Kate stopped walking and extended her hand to his arm, inciting him to do the same. "Do you think that's how she would respond if she had nothing to do?"

He shrugged again. "Elizabeth is one of the brightest people in this city. I wouldn't want her brain wasted on kitchen duty or something. Negotiating is what Elizabeth was born to do. She told me that she didn't get to travel off Atlantis much. I think she enjoys it."

Kate nodded again. "She's told me as much. John, let me ask you. Off the record, just as a friend. Are you and Elizabeth having any problems?"

He frowned. "No, not at all! What makes you ask that?"

"When someone loses a marriage mate, there are always very strong emotions that come with the grieving process. I'm just worried that, because of losing her John but finding you, perhaps those emotions have been suppressed. That she hasn't fully mourned the loss of her husband because she immediately found solace in you. Does that make any sense?"

He let her words sink in, processing the thoughts. "Yeah," he slowly answered. "It does."

She gave him a small smile, then gripped his elbow. "Maybe the three of us can discuss it sometime. I was going to bring it up during my next session with Elizabeth, but it might be helpful if you're there. Maybe give her a chance to really say goodbye."

Despite his confusion at how his presence would allow her to let go of her husband, he nodded. "Sure, if that's okay with Elizabeth."

"Of course," Kate agreed. "Well, our next session isn't until she returns from her mission, but we'll talk soon. Thanks, John," she said, resuming her walk for the cafeteria.

John, for his part, remained firmly rooted in place for a moment, still contemplating her words. He gradually dismissed them with a shake of his head, then switched directions and headed for his wife's office.

* * *

Eyes focused on her laptop, elbow on the table, hand supporting her chin. It felt second nature to her. It was one of the more comfortable positions that she took up while she was working. Her office wasn't as lavish as it used to be, just a smaller set of quarters near a lab that had been converted into a room for her. Desk and chairs were all she needed.

It wasn't that she missed her old office. The situation still just seemed surreal to her.

She glanced up at the familiar sound of boots scraping the floor at the entrance to her office.

"Hey," she greeted, smiling up at John.

"Hey yourself. What are you up to?" he asked, walking around behind her desk. Using his arms to brace himself, he leaned over her, gently kissing her temple as he looked at her computer screen.

She sighed. "I surrender," she said, clicking on the screen and downsizing the Solitaire game that she had been playing.

He laughed. He sat on the edge, right next to her, and softly touched her shoulder. "Sorry I wasn't there this morning."

"I forgive you," she said mockingly. "In any case, I'm sure you had your hands busy this morning. How was the training session?"

He shrugged. "Good. Nobody crashed, and only one person freaked out this morning. Still not on the scale of Carson, but …"

Elizabeth nodded. Everything until their arrival on Atlantis was symmetrical between the timelines, and she remembered with a flash of panic that if Carson had panicked even more than he had, they may not have been standing here at all. She didn't know why, but for some reason, that little reminder burrowed itself into her mind.

John must have seen the gloom settle over her. He rubbed her shoulder again. "You okay?" he asked quietly in concern.

She shook her head in the affirmative, then let out a little sigh. "I'm all right," she replied, trying to put on her most convincing smile.

But who was she trying to fool?

The man standing in front of her, no matter what universe he was from, still knew her better than she knew herself.

John gave her a knowing look. "Maybe … maybe we should talk to Heightmeyer," he told her slowly, sounding as if he was still unsure about the idea.

"I have a session with Kate tomorrow. I'll talk to her then."

"No," John said.

She looked curiously at him.

"I meant, _we_ should talk to her. Together."

Elizabeth frowned humorously. "What, like couples therapy?" she asked, teasing.

John's face didn't change.

The humor of the situation fled quickly. "John, you're worrying me."

"I'm worrying myself," he replied frankly. He reached for the small hands clasped over her laptop and held them, turning them every so often in examination. "After you came here, we kinda slipped back into our old lives. Sure, you're from another reality. Everybody knows that." He sighed heavily, then his earnest hazel eyes floated back to look at her green ones. "But it still feels like there's a couple of elephants in the room that we haven't directly acknowledged."

She looked at him, mouth slightly gaping, before she caught herself. "You mean, that my John is dead, and so is your Elizabeth."

He didn't shake his head. Instead, he just blinked.

She closed her eyes, then leaned back in her chair, letting her hands slip out of his. "When I was first put in command of this Expedition, I never expected this scenario."

"Well, you probably didn't expect life sucking aliens that use hands instead of fangs, either," he retorted, a smile pulling at the corner of his mouth.

She tilted her head. "True."

John groaned, then stood up. "Tell you what. I'm gonna go take a shower, then I've got some reports to sign off on. We'll have lunch, and you go to 529, and then we'll…"

"We'll what?"

He smirked. "We'll cross that bridge when we get there."

She smiled, then nodded in acceptance. "All right. Well, I have a little more reading to do about this world, so … I'll see you for lunch? 1200?"

"Sounds good," he answered as he started to leave.

She saw the silhouette start to fade, and was about to open her laptop again when he rushed back to her side, sat down on the desk again and held her head.

"Forgot something," was his only explanation as he pressed his lips to hers, kissing her deeply, softly, then drew back.

In a quick whisper, she murmured, "I don't really need to read the rest of that report."

He smirked. "Yeah, you do."

She moaned as he stood and walked towards the door. "See ya later."

"Bye."

With the tingling sensation still vibrating through her, she forced herself to steer her attention back to her work … and not to what she and John could be doing right now.

An exhale left her nose.

"And back to work," she told herself.


	4. Losing It

Sorry for the delay in posting this story, the particular muse bunny for this fic went on an extended vacation!

Read, review, and I hope you enjoy!

* * *

She wanted to cry.

But she was Doctor Elizabeth Weir.

She didn't cry.

Instead, she sifted through piles of paperwork, glared at computer screens, and drank coffee like her life depended on imbibing the hot bitter liquid. At this moment of internal turmoil, the coffee was the only constant. It was always strong, never changing.

Unless someone switched to decaf. Then life on Atlantis would end.

She groaned, running a hand over her face and leaning back in the office chair. At what point in her life did it get this crazy? When had she shifted so easily, so seamlessly into this life, that she forgot that this wasn't really her life?

For a fleeting moment, she almost wished that she had died on her Atlantis. Along with her husband.

She glanced up, hearing the military boots walking outside her presently closed office door. Knowing that he might walk through the door at any given minute almost made her recoil in fear, and that veiled reaction almost made her sick to her stomach. It was heinously ironic; she had a life here, she had a husband, and yet she was terrified that she might see him soon.

She wondered if her counterpart would roll over in her grave at the knowledge of that.

She sighed.

Then the doors opened.

John Sheppard slowly entered the small office, hands shoved into the pant pockets of his black fatigues. The doors closed behind him slowly, solemnly, as if they had knowledge of the conversation about to happen.

"I can't believe I'm saying this," he started slowly, staring at the toes of his black boots, "but we need to talk."

She closed her eyes, taking a deep breath, and clasped her hands on top of the desktop. "I know."

He took a seat in front of her desk, wincing as he made contact with the hard plastic seat. The sight was oddly reminiscent of how he used to sit in her office in the control room, wanting to –

Elizabeth withheld another sigh. It wasn't him. Their DNA might match, they might look exactly the same with the exception of a few grey hairs, but the handsome man in front of her wasn't the same man that she married.

It was getting harder and harder to remember every minute.

"It's getting harder to remember," John finally said, glancing up from under heavy eyes. The wrinkles became more obvious every day, a silent reminder of everything that he had gone through in this life. The difference between not being the military commander and taking on that heavy responsibility unexpectedly was evident. "I mean, I know that you're not her, but seeing you every day, waking up next to you, I start to forget."

"When I look at you," Elizabeth replied evenly, "it's like nothing has changed. And yet, the world is a completely different place." Her green eyes slowly looked up, meeting his uneasy gaze. "It's not even my world anymore," she added in a whispered voice.

John groaned, leaning back in his chair, not wanting to speak the words but knowing someone had to. It might as well be him. "Maybe this isn't such a good idea after all."

"What other option do I have, John? My Atlantis was destroyed! My husband is _dead_! And now I'm stranded in another world, left to pick up the pieces!" she shouted, standing from her desk, a tear threatening the corners of her eyes.

The lieutenant colonel stood as well, his arms crossed against his flat torso. "And I'm a piece that doesn't fit," he flatly stated, glaring at a vague point on the wall behind Elizabeth.

Her eyes darkened in resentment. "I didn't say that."

"You didn't have to," he replied, oddly calm.

"What are you talking about, John?"

"When Elizabeth was taken by the Replicators, all I wanted to do was find her. When I finally did, she wasn't Elizabeth anymore. At least, I didn't think she was." He looked up, his face flushed with shame. "I couldn't accept her because she had the body of a Replicator. I couldn't see past that long enough to realize that it was the same Elizabeth Weir that I trusted with my life … until she sacrificed herself to save us. I was too late," he admitted, rocking forward on his feet.

"John."

He looked up at her again, hazel eyes darkening as they looked hard at her. "That was three weeks before you showed up."

Elizabeth closed her eyes. She knew that John had lost his wife, but she had forgotten how recently it was. The memory of her loss was still fresh in his mind, the cuts not yet healed. She sighed in desperation, wanting things to miraculously heal between them.

But this was real life, not a Disney movie. Miracles didn't happen.

John groaned, unfolding his arms and running a hand through his untamed hair. "Woolsey's got a mission to a trading planet, asked for Lorne's team to go along as backup," he said, confusing Elizabeth.

_Why would he bring that up?_

"I think I'll join them. Might be a good time to do a performance review on the major."

_Oh. That's why._

Elizabeth nodded out of habit. She was giving him permission, as though he were still under her leadership, but this consent was different. Even though neither of them would say it aloud, they both knew what they were agreeing to: a trial separation.

Ironic, considering that they never had actually married each other.

John nodded decisively, and she knew that he had nothing more to say.

By the time that she had sat down, staring at the pile of paperwork in the corner of her desk, the doors had already shut behind him.

* * *

As it turned out, there was a monsoon on the planet.

Woolsey and SGA-2 stayed home.

John Sheppard only got more irritable.

Elizabeth's words had pierced his defenses, just like they did any time that she spoke to him. He always put up a shield, tried to ward people off from getting under his skin, but he always let his guard down around her. Inadvertently or on purpose, she was the only person in the world who could understand him.

It irritated the crap out of him right now.

Night had fallen about an hour ago. He had skipped dinner, instead opting for a grueling run around the outer piers of the city. A distraction was in order; anything would work. He had even considered offering to let Ronan and Teyla beat the crap out of him together, but Keller would only raise too many questions before sending him to Heightmeyer's office.

He grimaced as he rounded a corner. Kate Heightmeyer, the one that he had known, had died over a year ago. Just like Carson's clone when he was found, she was able to resume her life. Yeah, it was awkward, but they both managed to pull it off without a hitch.

He wasn't good at dealing with his feelings, which was one of the reasons why he was never able to be close with the psychiatrist.

And then Elizabeth Weir came back from the dead as well.

Only it wasn't his Elizabeth.

John Sheppard was convinced that the universe was definitely out to get him.

His running shoes thudded heavier and heavier with every step, echoing down the empty hallways. The same path was always taken: he would run to the extremity of the large pier, jog back into the center of the city, and proceed to the next available hallway. He was able to identify certain marks in hallways, and he would know if he had been here before, either while running or when Rodney found something that he just had to see before he blew it up.

Another grey wall presented itself and as John began to turn, he found himself face to face with Ronan Dex.

John jumped and skidded, slowing himself down before he ran into the imposing Satedan. "Hey, buddy," he greeted half-heartedly, panting as he leant against the wall.

Ronan only nodded at him. "You tryin' to kill yourself?"

"Yeah. You got a problem with that?" he shot back.

Ronan shrugged in the affirmative. "If you collapse out here, no one will find you for weeks. McKay will find your secret stash."

John chuckled sardonically. "Let him. What do I care?"

More silence.

"You wanna keep going?"

This was the reason they got along so well: Ronan didn't like to talk either.

They continued running around the city, going over an archway bridge that connected one of the taller spiraling towers to the main passageway back into the heart of the city. At this point, he didn't care if his legs were going to kill him in the morning. He kept pushing harder and harder, leaving Ronan behind in a corridor at one point.

They jogged down a staircase and John glanced up at the signage above the entryway, locating themselves in the section.

He abruptly stopped running, bracing his hands against the grey steel wall he ran into.

"What's wrong?" Ronan asked, his tone a mixture of concern and annoyance.

"This is it," Sheppard replied in a low whisper. "This is the storage room where they found her."

He walked uncertainly to the door, slowly running his hand over the control crystal.

The doors opened and he unhurriedly stepped in, Ronan following a few paces behind him. He automatically reached for his stunner upon seeing the suspiciously dark interior, but groaned when he found no holster.

John smirked, then surveyed the room.

Along with their teams, Rodney and Zelenka had spent most of their spare time during the past two months analyzing and cataloging the items in the room. Despite the wide variety, his attention was only drawn to the reflective device at the end of the second aisle, seemingly supporting itself with a narrow base.

John stood in front of it, a contemplative gaze on his face. He still wasn't sure if he loved or hated the device.

"This is stupid," Ronan voiced. "Weir is back. What difference does it make if she's from another reality?"

"That's what I've been asking myself," John replied, reaching out to touch the control interface that McKay had identified on the side of the arch. He knew it wouldn't do anything; after Elizabeth and Kate came through, an apparent explosion on the other side had destroyed what was left of that room, as well as the mirror device. Having no other terminal, it wouldn't connect. He chuckled, turning back to look at Ronan. "And I still can't answer it. It's just … geez. I know you're touchy about this, but let's say it wasn't Elizabeth. What if it was your wife and son from another reality that came through?"

From the raised eyebrows and widened eyes, John could tell that he had thrown Ronan for a loop. "What if you were in my shoes? What would you do?"

Slowly, Ronan shrugged again, staring at his boots. "I'd welcome them back. Pick up where we left off."

"So why can't I do that with Elizabeth?"

Ronan groaned. "Sheppard, my wife and son have been dead for years. We'd have to start over." He looked up pointedly at his friend. "She was only dead for three weeks when she came back again. You didn't start over. You just kept going."

John sighed, closing his eyes. He bent forward, covering his face with his hands. _When did Ronan get so chatty? _"All right. So what you're saying is that I have to forget everything that happened with _my_ Elizabeth? With _my _wife?"

"No."

"Then what are you sayin', Ronan? Cause right now, you're making as much sense as McKay without coffee."

"You're basing your life with this Weir on the one you had before. But those memories are yours. Not hers." Ronan nodded to him, then turned and walked towards the doors.

"Where you going?"

"I'm leaving. Too much talking, not enough hitting."

"But I-"

"You keep bragging to McKay how smart you are. I'm sure you'll figure it out."

The doors shut behind Ronan, leaving John with a broken mirror in a dark room.

* * *

Thanks for reading, I will do my best to have a new chapter posted within a few weeks!


	5. Starting Over

Sorry I was away for so long!

After a debate with the fic bunnies, we decided to tie up the loose string and complete the story - at least for now. After I get closer to completion with my two primary Sparky stories, I may revisit this one, as well as "Atlantis Orientation" and post a few extra chapters, but I thought for now, "all good things" ...

Thank you for reading! Long live Sparky!

* * *

The first thing she noticed that was unusual was the sunlight coming in the windows on her left instead of her right.

Then she noticed the Johnny Cash poster hanging on the wall.

Somehow, during the night, she had left her old quarters and made her way into the bedroom that she and John had been sharing. She had fallen tranquilly asleep in his bed.

Without him.

She didn't feel like a stranger, but she still felt strange. John had wanted to get her out of the guest quarters that she had been placed in, even if it meant bringing her last memories of home with her. She found it easy to settle into a new life here. Too easy, in fact. The fact that she had lost her temper and gone off on him yesterday was ample evidence of that.

Elizabeth sighed, then glanced at the alarm clock on the other side of the bed.

John was leaning forward in a chair, bent elbows resting on his bent knees, clad only in a pair of flannel sleep pants.

Her eyes widened. "Oh," she murmured hastily, moving to get out of bed and escape the quarters.

Hearing her gasp, John looked up, dark circles under his eyes. He held up a hand. "No, no, it's okay." He stood from his seat and walked to the bed, sitting down on the edge, close to her. "I, uh, I thought you wouldn't want to stay here after, well, you know."

"I didn't," she replied, looking down at the blue plaid pattern on his pants. "I went to my quarters. But I couldn't sleep, and I wound up back here." She glanced up at him, slightly embarrassed. "Were you here?"

He nodded. "Yeah. I couldn't sleep either," he told her with a shrug, "so I took a shower. When I got out, you were in the bed, sound asleep." He smiled softly. "I didn't wanna bother you."

"John, did you sleep in the chair all night?"

"No. I slept on the sofa."

She sighed, and then sat up in bed, matching John's eye level. "About yesterday, I-"

"I overreacted," he said quickly, before she could finish.

She blinked, then frowned. "John, you barely said anything harsh during the argument. I don't think you're to blame."

"I was too quick to find a way to give us a break. I shouldn't have brought up Elizabeth."

Elizabeth grinned wryly. "I think that's going to be an issue, no matter what."

"Yeah, I suppose." He brought his finger to her chin, tilting it up. "I'm sorry."

She allowed a small smile. "Me too."

"Let's start over."

She frowned again. "What do you mean?"

"Well, you're Elizabeth, but you're not _my_ Elizabeth. And the only way we're gonna get past that is if we start doing our own thing, right here, right now. So I thought that we should start over." To facilitate this, he extended his hand. "Hi. I'm John."

She extended her small graceful hand towards his as he took it. "Elizabeth."

"Well, it's very nice to meet you, Elizabeth. Would you like to go to dinner sometime?"

Her eyes twinkled. "Actually, I'd prefer breakfast in bed," she replied, hoping that he would catch her drift.

He leaned forward and captured her lips with his, answering her unspoken question as he pushed her gently down in the bed with the New Lantean sun streaming through the windows behind them.

* * *

Thank you again for reading!


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